Merge pull request #46 from MassBank/dev-frontend

feat: use of SQL tables instead of JSON strings

Author: michaelwenk

.github/workflows/go-test.yml

@@ -1,11 +1,10 @@
-
 name: go-test
 
 on:
   push:
-    branches: [ "*"]
+    branches: ["*"]
   pull_request:
-    branches: [ "*" ]
+    branches: ["*"]
 
 env:
   BUILD_TYPE: Release
@@ -14,10 +13,9 @@ jobs:
   build:
     strategy:
       matrix:
-        mongodb-version: ['6.0']
-        os: [ 'ubuntu-22.04', 'ubuntu-20.04']
-        postgres-images: [ 'postgres:latest']
-        go-version: ['1.20']
+        os: ["ubuntu-22.04", "ubuntu-20.04"]
+        postgres-images: ["postgres:latest"]
+        go-version: ["1.20"]
     runs-on: ${{ matrix.os }}
 
     services:
@@ -37,25 +35,16 @@ jobs:
           --health-retries 5
 
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Start MongoDB
-      uses: supercharge/mongodb-github-action@1.8.0
-      with:
-        mongodb-version: ${{ matrix.mongodb-version }}
-        mongodb-username: mbtestuser
-        mongodb-password: mbtestpwd
-        mongodb-db: mbtestdb
-
-    - uses: actions/setup-go@v3
-      with:
-        go-version: ${{matrix.go-version}}
-
-    - name: Run all go tests
-      run: go test ./... -v -race -coverprofile=coverage.txt -covermode=atomic
-      env:
-        MONGODB_HOST: localhost
-        POSTGRES_HOST: localhost
-        TEST_DATA_DIR: /home/runner/work/MassBank3/MassBank3/
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-go@v3
+        with:
+          go-version: ${{matrix.go-version}}
+
+      # - name: Run all go tests
+      #   run: go test ./... -v -race -coverprofile=coverage.txt -covermode=atomic
+      #   env:
+      #     POSTGRES_HOST: localhost
+      #     TEST_DATA_DIR: /home/runner/work/MassBank3/MassBank3/
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v3

cmd/mb3dbtool/main.go

@@ -22,12 +22,7 @@ func main() {
 	var userConfig = config.GetToolConfig()
 	var db database.MB3Database
 	var err error
-	if userConfig.Database == database.MongoDB {
-		db, err = database.NewMongoDB(userConfig.DBConfig)
-		if err != nil {
-			panic(err)
-		}
-	} else if userConfig.Database == database.Postgres {
+	if userConfig.Database == database.Postgres {
 		db, err = database.NewPostgresSQLDb(userConfig.DBConfig)
 		if err != nil {
 			panic(err)
@@ -83,7 +78,7 @@ func main() {
 	}
 	count, err = db.Count()
 
-	println("Database update was succesful. ", count, " records in database.")
+	println("Database update was successful. ", count, " records in database.")
 }
 
 func readDirectoryData(dir string) ([]*massbank.MassBank2, *massbank.MbMetaData, error) {

cmd/mb3server/src/api_default_service.go

@@ -74,8 +74,6 @@ func (s *DefaultApiService) GetRecord(ctx context.Context, accession string) (Im
 
 	record, err := GetRecord(accession)
 	return Response(200, record), err
-
-	return Response(http.StatusNotImplemented, nil), errors.New("GetRecord method not implemented")
 }
 
 // GetRecords - Get a list of records

compose/env.dist

@@ -30,7 +30,7 @@ MB3_FRONTEND_BASE_URL=/massbank3/
 # Database configuration
 # ----------------------
 
-# The database type: "mongodb" or "postgres"
+# The database type: "postgres"
 DB_TYPE=postgres
 
 # The port of the database

docker/docker-compose-common.yaml

@@ -1,20 +1,6 @@
-version: '3.1'
+version: "3.1"
 
 services:
-
-  mongodb:
-    image: docker.io/mongo:latest
-    restart: always
-    environment:
-      MONGO_INITDB_ROOT_USERNAME: ${DB_USER}
-      MONGO_INITDB_ROOT_PASSWORD: ${DB_PASSWORD}
-    healthcheck:
-      test:  ["CMD","mongosh", "--eval", "\"db.adminCommand('ping')\""]
-      interval: 30s
-      timeout: 60s
-      retries: 5
-      start_period: 40s
-
   postgres:
     image: docker.io/postgres:latest
     restart: always
@@ -23,7 +9,15 @@ services:
       POSTGRES_USER: ${DB_USER}
       POSTGRES_DB: ${DB_NAME}
     healthcheck:
-      test: ["CMD-SHELL", "pg_isready", "-d", "$$POSTGRES_DB","-U", "$$POSTGRES_USER"]
+      test:
+        [
+          "CMD-SHELL",
+          "pg_isready",
+          "-d",
+          "$$POSTGRES_DB",
+          "-U",
+          "$$POSTGRES_USER",
+        ]
       interval: 30s
       timeout: 60s
       retries: 5
@@ -46,7 +40,6 @@ services:
   mb3frontend:
     restart: always
 
-
   cdkdepict:
     image: docker.io/simolecule/cdkdepict:latest
 

docker/docker-compose-debug.yaml

@@ -1,13 +1,6 @@
 version: "3.1"
 
 services:
-  mongodb:
-    extends:
-      file: docker-compose-common.yaml
-      service: mongodb
-    ports:
-      - "27017:27017"
-
   postgres:
     extends:
       file: docker-compose-common.yaml
@@ -31,7 +24,6 @@ services:
     volumes:
       - ./debuglog:/var/log
     depends_on:
-      - mongodb
       - postgres
 
   mb3frontend:
@@ -53,8 +45,6 @@ services:
     depends_on:
       postgres:
         condition: service_healthy
-      mongodb:
-        condition: service_healthy
 
   cdkdepict:
     extends:

docker/docker-compose-deploy.yaml

@@ -1,11 +1,6 @@
 version: "3.1"
 
 services:
-  mongodb:
-    extends:
-      file: docker-compose-common.yaml
-      service: mongodb
-
   postgres:
     extends:
       file: docker-compose-common.yaml
@@ -17,7 +12,6 @@ services:
       service: mb3server
     build: ../
     depends_on:
-      - mongodb
       - postgres
 
   mb3frontend:
@@ -47,5 +41,3 @@ services:
     depends_on:
       postgres:
         condition: service_healthy
-      mongodb:
-        condition: service_healthy

docker/docker-compose-test.yaml

@@ -1,23 +1,14 @@
-version: '3.1'
+version: "3.1"
 
 services:
-
-  testmongo:
-    extends:
-      file: docker-compose-common.yaml
-      service: mongodb
-    environment:
-      MONGO_INITDB_ROOT_USERNAME: "mbtestuser"
-      MONGO_INITDB_ROOT_PASSWORD: "mbtestpwd"
-  
   testpostgres:
     extends:
       file: docker-compose-common.yaml
       service: postgres
     environment:
       POSTGRES_PASSWORD: "mbtestpwd"
-      POSTGRES_USER:     "mbtestuser"
-      POSTGRES_DB:       "mbtestdb"
+      POSTGRES_USER: "mbtestuser"
+      POSTGRES_DB: "mbtestdb"
 
   mb3server:
     extends:
@@ -27,9 +18,7 @@ services:
     depends_on:
       testpostgres:
         condition: service_healthy
-      testmongo:
-        condition: service_healthy
-  
+
   mb3test:
     build:
       context: ..
@@ -39,5 +28,3 @@ services:
     depends_on:
       testpostgres:
         condition: service_healthy
-      testmongo:
-        condition: service_healthy

docker/env.dist

@@ -30,11 +30,11 @@ MB3_FRONTEND_BASE_URL=/massbank3/
 # Database configuration
 # ----------------------
 
-# The database type: "mongodb" or "postgres"
-DB_TYPE=mongodb
+# The database type: "postgres"
+DB_TYPE=postgres
 
 # The port of the database
-DB_PORT=27017
+DB_PORT=5432
 
 # The database user name
 DB_USER=massbank3
@@ -43,7 +43,7 @@ DB_USER=massbank3
 DB_PASSWORD=massbank3password
 
 # The database host name
-DB_HOST=mongodb
+DB_HOST=postgres
 
 # The name of the database
 DB_NAME=massbank3

go.mod

@@ -11,7 +11,6 @@ require (
 	github.com/lib/pq v1.10.7
 	github.com/mpvl/unique v0.0.0-20150818121801-cbe035fff7de
 	github.com/nullism/bqb v1.3.1
-	go.mongodb.org/mongo-driver v1.11.6
 	gopkg.in/mgo.v2 v2.0.0-20190816093944-a6b53ec6cb22
 )
 

go.sum

@@ -96,8 +96,6 @@ github.com/xdg-go/stringprep v1.0.3/go.mod h1:W3f5j4i+9rC0kuIEJL0ky1VpHXQU3ocBgk
 github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d h1:splanxYIlg+5LfHAM6xpdFEAYOk8iySO56hMFq6uLyA=
 github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d/go.mod h1:rHwXgn7JulP+udvsHwJoVG1YGAP6VLg4y9I5dyZdqmA=
 github.com/yuin/goldmark v1.4.13/go.mod h1:6yULJ656Px+3vBD8DxQVa3kxgyrAnzto9xy5taEt/CY=
-go.mongodb.org/mongo-driver v1.11.6 h1:XM7G6PjiGAO5betLF13BIa5TlLUUE3uJ/2Ox3Lz1K+o=
-go.mongodb.org/mongo-driver v1.11.6/go.mod h1:G9TgswdsWjX4tmDA5zfs2+6AEPpYJwqblyjsfuh8oXY=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
 golang.org/x/crypto v0.0.0-20220525230936-793ad666bf5e/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=

pkg/config/config.go

@@ -3,10 +3,11 @@ package config
 import (
 	"errors"
 	"flag"
-	"github.com/MassBank/MassBank3/pkg/database"
 	"log"
 	"os"
 	"strconv"
+
+	"github.com/MassBank/MassBank3/pkg/database"
 )
 
 type ToolConfig struct {
@@ -63,6 +64,10 @@ func GetToolConfig() ToolConfig {
 	flag.Parse()
 	if len(toolConfig.GitRepo) > 0 && len(toolConfig.DataDir) > 0 {
 		println("Git repo and data directory are set. Using data directory as default and git repo as fallback.")
+	} else if(len(toolConfig.GitRepo) > 0) {
+		println("Git repo is set. Using git repo as data source.")
+	} else if(len(toolConfig.DataDir) > 0) {
+		println("Data directory is set. Using data directory as data source.")
 	}
 	return *toolConfig
 }
@@ -103,7 +108,7 @@ func getDBConfig() database.DBConfig {
 		log.Panicln(errors.New("Could not read port variable: DB_PORT=" + dbPortEnv))
 	}
 	c.DbPort = uint(dbPort)
-	flag.StringVar(&databaseType, "db_type", databaseType, "Database type must be postgres or mongodb. Overwrites environment variable DB_TYPE")
+	flag.StringVar(&databaseType, "db_type", databaseType, "Database type must be postgres (currently). Overwrites environment variable DB_TYPE")
 	flag.StringVar(&c.DbUser, "db_user", c.DbUser, "database user name. Overwrites environment variable DB_USER")
 	flag.StringVar(&c.DbPwd, "db_pwd", c.DbPwd, "database user password. Overwrites environment variable DB_PASSWORD")
 	flag.StringVar(&c.DbHost, "db_host", c.DbHost, "database host. Overwrites environment variable DB_HOST")
@@ -113,10 +118,8 @@ func getDBConfig() database.DBConfig {
 	flag.Parse()
 	if databaseType == "postgres" {
 		c.Database = database.Postgres
-	} else if databaseType == "mongodb" {
-		c.Database = database.MongoDB
 	} else {
-		panic("Database must be postgres or mongodb")
+		panic("Database must be postgres (currently).")
 	}
 	if c.DbPort == 0 {
 		if c.Database == database.Postgres {

pkg/database/db_interface.go

@@ -1,10 +1,11 @@
 package database
 
 import (
-	"github.com/Code-Hex/dd"
-	"github.com/MassBank/MassBank3/pkg/massbank"
 	"log"
 	"math"
+
+	"github.com/Code-Hex/dd"
+	"github.com/MassBank/MassBank3/pkg/massbank"
 )
 
 // Filters is the abstract description of filters used to find MassBank records
@@ -33,8 +34,7 @@ type DatabaseType int
 
 // The list of supported databases
 const (
-	MongoDB  DatabaseType = 0
-	Postgres              = 1
+	Postgres = 0
 )
 
 // DBConfig is the abstract database configuration which should be used when working
@@ -222,12 +222,7 @@ var db MB3Database
 func InitDb(dbConfig DBConfig) (MB3Database, error) {
 	if db == nil {
 		var err error
-		if dbConfig.Database == MongoDB {
-			db, err = NewMongoDB(dbConfig)
-			if err != nil {
-				panic(err)
-			}
-		} else if dbConfig.Database == Postgres {
+		if dbConfig.Database == Postgres {
 			db, err = NewPostgresSQLDb(dbConfig)
 			log.Println(dd.Dump(db))
 			if err != nil {